To determine the incidence of genetic heterogeneity in primary prostate cancer, we have microdissected 125 tumor and mesenchymal foci from 18 patient biopsies and analyzed the DNA for loss of heterozygosity using PCR microsatellite markers. In 100% of patients with genetic lesions on chromosome 8p, there was evidence for intratumoral genetic heterogeneity. There was also a low but significant incidence of loss of heterozygosity in mesenchymal tissue. Our results show that phenotypically similar tumor foci can have different genotypes and provide evidence for the multifocality of tumor development in the prostate.